The executive credited with steering the MTA back on track after an embarrassing accounting scandal will resign to make way for a new administration to be appointed by Gov.-elect Eliot Spitzer.

Katherine Lapp, the Metropolitan Transportation Authority’s executive director, oversaw the agency after accusations that the transit giant had two sets of books – one for the boardroom and one for the public – at a time when fares were being hiked.

During her five years at the controls, Lapp made a mission of gaining the public’s confidence.

Lapp said she spoke with Spitzer and agreed that she would run the agency through the end of the year.

Across the tracks, the fate of Transport Workers Union President Roger Toussaint may be resolved today, when election ballots are tallied.

Toussaint spent five days in jail for leading last year’s illegal three-day Christmas-season strike, a walkout that cost the union $2.5 million in fines.

Meanwhile, the Port Authority yesterday approved a $5.7 billion budget for next year, including $661 million for World Trade Center infrastructure.